Tuple

About: Tuple is a research topic. Over the lifetime, 6513 publications have been published within this topic receiving 146057 citations. The topic is also known as: tuple & ordered tuplet.

An Evolutionary Model for Protein-Coding Regions with Conserved RNA Structure

Abstract: Here we present a model of nucleotide substitution in protein-coding regions that also encode the formation of conserved RNA structures. In such regions, apparent evolutionary context dependencies exist, both between nucleotides occupying the same codon and between nucleotides forming a base pair in the RNA structure. The overlap of these fundamental dependencies is sufficient to cause "contagious" context dependencies which cascade across many nucleotide sites. Such large-scale dependencies challenge the use of traditional phylogenetic models in evolutionary inference because they explicitly assume evolutionary independence between short nucleotide tuples. In our model we address this by replacing context dependencies within codons by annotation-specific heterogeneity in the substitution process. Through a general procedure, we fragment the alignment into sets of short nucleotide tuples based on both the protein coding and the structural annotation. These individual tuples are assumed to evolve independently, and the different tuple sets are assigned different annotation-specific substitution models shared between their members. This allows us to build a composite model of the substitution process from components of traditional phylogenetic models. We applied this to a data set of full-genome sequences from the hepatitis C virus where five RNA structures are mapped within the coding region. This allowed us to partition the effects of selection on different structural elements and to test various hypotheses concerning the relation of these effects. Of particular interest, we found evidence of a functional role of loop and bulge regions, as these were shown to evolve according to a different and more constrained selective regime than the nonpairing regions outside the RNA structures. Other potential applications of the model include comparative RNA structure prediction in coding regions and RNA virus phylogenetics.

Opinion Extraction Using a Learning-Based Anaphora Resolution Technique

Abstract: This paper addresses the task of extracting opinions from a given document collection. Assuming that an opinion can be represented as a tuple 〈Subject, Attribute, Value〉, we propose a computational method to extract such tuples from texts. In this method, the main task is decomposed into (a) the process of extracting Attribute-Value pairs from a given text and (b) the process of judging whether an extracted pair expresses an opinion of the author. We apply machine-learning techniques to both subtasks. We also report on the results of our experiments and discuss future directions.

Relational specifications of infinite query answers

Abstract: We investigate here functional deductive databases: an extension of DATALOG capable of representing infinite phenomena. Rules in functional deductive databases are Horn and predicates can have arbitrary unary and limited k-ary function symbols in one fixed position. This class is known to be decidable. However, least fixpoints of functional rules may be infinite. We present here a method to finitely represent infinite least fixpoints and infinite query answers as relational specifications. Relational specifications consist of a finite set of tuples and of a finitely specified congruence relation. Our method is applicable to every domain-independent set of functional rules.

Data Mining in Large Databases Using Domain Generalization Graphs

Abstract: Attribute-oriented generalization summarizes the information in a relational database by repeatedly replacing specific attribute values with more general concepts according to user-defined concept hierarchies. We introduce domain generalization graphs for controlling the generalization of a set of attributes and show how they are constructed. We then present serial and parallel versions of the Multi-Attribute Generalization algorithm for traversing the generalization state space described by joining the domain generalization graphs for multiple attributes. Based upon a generate-and-test approach, the algorithm generates all possible summaries consistent with the domain generalization graphs. Our experimental results show that significant speedups are possible by partitioning path combinations from the DGGs across multiple processors. We also rank the interestingness of the resulting summaries using measures based upon variance and relative entropy. Our experimental results also show that these measures provide an effective basis for analyzing summary data generated from relational databases. Variance appears more useful because it tends to rank the less complex summaries (i.e., those with few attributes and/or tuples) as more interesting.